@@ -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: 1.1.3

+Version: 1.1.4

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

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

          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase

@@ -89,3 +89,7 @@ test_GmapGenome_spliceSites_replacement <- function() {

   x <- spliceSites(genome, name="dbSnp") <- shiftedExons

   checkIdentical(class(x), class(GRangesList()))

 }

+

+test_if_GmapGenome_dir_does_not_exist <- function() {

+  checkException(GmapGenome(genome="NoGenome", directory = file.path(tempdir(), "DoesNotExist")))

+}

new file mode 100644

@@ -0,0 +1,7 @@

+test_IITs_not_created <- function() {

+  gmapGenome <- GmapGenome(genome="NoGenome", directory = getwd())

+  btp <- BamTallyParam(genome=gmapGenome,

+                       which = RangesList())

+  bam_file <- system.file("extdata/test_data_aln/test_data_aln.concordant_uniq.bam", package="gmapR", mustWork=TRUE)

+  checkException(bam_tally(x=bam_file, param=btp))

+}