@@ -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: 1.5.6

+Version: 1.5.7

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

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

          GenomicFeatures, Biostrings, VariantAnnotation (>= 1.9.4), tools,

@@ -28,7 +28,7 @@ setClass("GsnapParam",

                         split_output = "logical",

                         terminal_threshold = "integer",

                         gmap_mode = "character",

-                        clip_overlaps = "logical",

+                        clip_overlap = "logical",

                         extra = "list"))

 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

@@ -160,7 +160,7 @@ GsnapParam <- function(genome, unique_only = FALSE, molecule = c("RNA", "DNA"),

                        terminal_threshold = if (molecule == "DNA") 1000L else 2L,

                        gmap_mode = if (molecule == "DNA") "none" else

                        "pairsearch,terminal,improve",

-                       clip_overlaps = FALSE, ...)

+                       clip_overlap = FALSE, ...)

 {

   if (missing(genome))

     stop("The 'genome' must be specified (should be coercible to GmapGenome)")

@@ -215,7 +215,7 @@ gsnapParam <- GsnapParam(genome=gmapGenome,

                          splicing="knownGene",

                          indel_penalty=1L,

                          distant_splice_penalty=1L,

-                         clip_overlaps=TRUE)

+                         clip_overlap=TRUE)

 @ 

 Now we are ready to align.