@@ -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: 0.99.7

+Version: 0.99.8

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

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

          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase

@@ -163,9 +163,9 @@ GsnapParam <- function(genome, unique_only = FALSE,

       params$snps <- GmapSnps(snps, genome)

     }

   }

-  extra <- params$...

+  dots <- list(...)

   ##TODO: this breaks if ... has anything in it

-  if (!missing(extra) && !is.null(names(extra))) {

+  if (length(dots) > 0) {

     params$extra <- params$...

   }

   params$... <- NULL

@@ -190,6 +190,11 @@ setAs("GsnapParam", "list", function(from) {

   }

   to$snpsdir <- path(directory(to$snps))

   to$snps <- NULL

+

+  extras <- to$extra

+  to <- c(to, extras)

+  to$extra <- NULL

+  

   to

 })