@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

     to work with GMAP and GSNAP from within R. In addition, it provides 

     methods to tally alignment results on a per-nucleotide basis using 

     the bam_tally tool.

-Version: 0.99.21

+Version: 0.99.22

 Depends: R (>= 2.15.0), methods, GenomicRanges

 Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges,

          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase

@@ -24,7 +24,7 @@ setMethod("length", "GmapSnpDirectory", function(x) {

 setReplaceMethod("snps", c("GmapSnpDirectory", "character", "VCF"),

                  function(x, name, genome = GmapGenome(genome(x)),

-                          iitPath = tempdir(), ..., value)

+                          iitPath = tempdir(), value)

                  {

                    gr <- rowData(value)

                    values(gr) <- values(fixed(value))[c("REF", "ALT")]

@@ -6,8 +6,10 @@ test_GmapGenome_constructor_DNAStringSet_noCreate <- function() {

 }

 test_GmapGenome_constructor_DNAStringSet_create <- function() {

-  dna <- Biostrings::DNAStringSet("ACTGTGTCAG")

-  names(dna) <- "test"

+  set.seed(1)

+  seq <- paste0(sample(c("A", "C", "G", "T"), 2000, replace=TRUE),

+                collapse="")

+  dna <- Biostrings::DNAStringSet(seq)

   genomeDir <- file.path(tempdir(), as.integer(runif(1) * 1000000000))

   if (file.exists(genomeDir)) unlink(genomeDir, recursive=TRUE)

   dir.create(genomeDir, recursive=TRUE)

@@ -7,6 +7,8 @@

 \alias{length,GmapSnpDirectory-method}

 \alias{names,GmapSnpDirectory-method}

 \alias{path,GmapSnpDirectory-method}

+\alias{snps<-,GmapSnpDirectory,character,VCF-method}

+\alias{snps<-,GmapSnpDirectory,character,character-method}

 \title{Class \code{"GmapSnpDirectory"}}

 \description{

@@ -25,8 +25,10 @@ Objects can be created by calls of the form \code{GmapSnps(snps,

   \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.}

-  }

+    argument does not exist, create it.}

+  \item{...}{Additional arguments to be passed to the SNPs

+    replacement method.}

+}

 \section{Accessors}{

     \describe{

@@ -36,8 +38,7 @@ Objects can be created by calls of the form \code{GmapSnps(snps,

 	this \code{GmapSnps} object.}

     }

 }

-

-  

+ 

 \section{Methods}{

   \describe{

     \item{directory}{\code{signature(x = "GmapSnps")}: ... }