@@ -1,7 +1,7 @@

 \name{gsnap-methods}

 \docType{methods}

 \alias{gsnap-methods}

-\alias{gsnap,character,characterORNULL,GsnapParam-method}

+\alias{gsnap,character,character_OR_NULL,GsnapParam-method}

 \alias{gsnap}

 \title{Align a Set of Reads Using the GSNAP Aligner}

@@ -15,7 +15,7 @@

 }

 \usage{

-\S4method{gsnap}{character,characterORNULL,GsnapParam}(input_a, input_b, params,

+\S4method{gsnap}{character,character_OR_NULL,GsnapParam}(input_a, input_b, params,

                    output = file.path(getwd(),

                                       file_path_sans_ext(basename(input_a),

                                                          TRUE)),

@@ -17,7 +17,8 @@

 \usage{

 \S4method{gsnap}{character,characterORNULL,GsnapParam}(input_a, input_b, params,

                    output = file.path(getwd(),

-                                      file_path_sans_ext(input_a, TRUE)),

+                                      file_path_sans_ext(basename(input_a),

+                                                         TRUE)),

                    consolidate = TRUE, ...)

 }

@@ -16,7 +16,8 @@

 \usage{

 \S4method{gsnap}{character,characterORNULL,GsnapParam}(input_a, input_b, params,

-                   output = file_path_sans_ext(input_a, TRUE),

+                   output = file.path(getwd(),

+                                      file_path_sans_ext(input_a, TRUE)),

                    consolidate = TRUE, ...)

 }

@@ -32,8 +32,8 @@

     will be saved in \code{dirname(output)}. If \code{split_output} in

     \code{params} is \code{TRUE}, \code{basename(output)} is used as the

     common stem for the multiple output files. Otherwise, the results

-    are saved to \code{output} with the \dQuote{bam} extension

-    appended.

+    are saved to a single SAM file, its path formed by adding the

+    \dQuote{sam} extention to \code{output}.

   }

   \item{consolidate}{If GSNAP is run with multiple worker threads, each

   thread will output its own set of files. If consolidate is set to

@@ -26,9 +26,15 @@

   is the only FASTA file used as input.}

   \item{input_b}{If provided, a path to the FASTA file containing the

   second set of reads from paired-end sequencing data.}

-  \item{params}{A \code{GsnapParam} object to configure the behavior of GSNAP.}

-  \item{output}{The output directory for the GSNAP alignments. If not

-  provided, the directory is the same directory that contains input_a.}

+  \item{params}{A \code{GsnapParam} object to configure the behavior of

+    GSNAP.}

+  \item{output}{The output path for the GSNAP alignments. The results

+    will be saved in \code{dirname(output)}. If \code{split_output} in

+    \code{params} is \code{TRUE}, \code{basename(output)} is used as the

+    common stem for the multiple output files. Otherwise, the results

+    are saved to \code{output} with the \dQuote{bam} extension

+    appended.

+  }

   \item{consolidate}{If GSNAP is run with multiple worker threads, each

   thread will output its own set of files. If consolidate is set to

   TRUE, these files will be merged. The default is TRUE.}

new file mode 100644

@@ -0,0 +1,43 @@

+\name{gsnap-methods}

+\docType{methods}

+\alias{gsnap-methods}

+\alias{gsnap,character,characterORNULL,GsnapParam-method}

+\alias{gsnap}

+

+\title{Align a Set of Reads Using the GSNAP Aligner}

+

+\description{

+  Given a set of alignments, align them to a genome using the GSNAP

+  algorithm. The GSNAP algorithm contains a number of features making it

+  a very high quality algorithm for dealing with short reads and those

+  from RNA-seq data in particular. Via the \code{GsnapParam} class

+  and the \code{gsnap} function, R users are given complete control over GSNAP.

+}

+

+\usage{

+\S4method{gsnap}{character,characterORNULL,GsnapParam}(input_a, input_b, params,

+                   output = file_path_sans_ext(input_a, TRUE),

+                   consolidate = TRUE, ...)

+}

+

+\arguments{

+  \item{input_a}{A path to the FASTA file containing reads to align against a

+  \code{GmapGenome} object. If the sequencing data is single-end, this

+  is the only FASTA file used as input.}

+  \item{input_b}{If provided, a path to the FASTA file containing the

+  second set of reads from paired-end sequencing data.}

+  \item{params}{A \code{GsnapParam} object to configure the behavior of GSNAP.}

+  \item{output}{The output directory for the GSNAP alignments. If not

+  provided, the directory is the same directory that contains input_a.}

+  \item{consolidate}{If GSNAP is run with multiple worker threads, each

+  thread will output its own set of files. If consolidate is set to

+  TRUE, these files will be merged. The default is TRUE.}

+  \item{...}{Additional arguments to pass to GSNAP not specifically

+  supported by the \code{gmapR} package.}

+}

+

+\value{

+  A \code{GsnapOutput} class.

+}

+

+\author{Michael Lawrence}