@@ -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: 0.99.26

+Version: 0.99.27

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

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

          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase

@@ -64,7 +64,7 @@ test_GmapGenome_spliceSites_replacement <- function() {

     eg <- org.Hs.egSYMBOL2EG[["TP53"]]

     txTP53 <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene,

                           vals = list(gene_id = eg))

-    rngs <- GRanges(ranges=IRanges(start(range(tx)), end(range(tx))),

+    rngs <- GRanges(ranges=IRanges(start(range(txTP53)), end(range(txTP53))),

                     seqnames="chr17")

     rngs + 1e6

   }