@@ -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: 0.99.19

+Version: 0.99.20

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

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

          GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase

@@ -58,7 +58,12 @@ GmapGenome <- function(genome,

   if (is(genome, "DNAStringSet")) {

     if (missing(name))

       stop("If the genome argument is a DNAStringSet object",

-           "the name argument must be provided") 

+           "the name argument must be provided")

+    if (is.null(names(genome))) {

+      stop("If the genome is provided as a DNAStringSet, ",

+           "the genome needs to have names. ",

+           "E.g., \"names(genome) <- someSeqNames")

+    }

   }

   if (!isSingleString(name))

     stop("'name' must be a single, non-NA string")

@@ -9,10 +9,12 @@ test_GmapGenome_constructor_DNAStringSet_create <- function() {

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

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

   dir.create(genomeDir, recursive=TRUE)

-  

   on.exit(unlink(genomeDir, recursive=TRUE))

+  checkException(GmapGenome(genome=dna, directory=genomeDir,

+                            name="thing", create=TRUE))

+  names(dna) <- "sampleDNAStringSet"

   gmapGenome <- GmapGenome(genome=dna, directory=genomeDir,

-                           name="thing", create=TRUE)                           

+                           name="thing", create=TRUE)

   checkTrue(is(gmapGenome, "GmapGenome"))

 }