@@ -9,12 +9,13 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

         methods 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: 1.13.8

+Version: 1.13.9

 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),

         GenomicRanges (>= 1.17.12)

-Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.31.2),

-        GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>= 1.11.4),

-        tools, Biobase, BSgenome, GenomicAlignments (>= 1.1.9), BiocParallel

+Imports: S4Vectors (>= 0.9.25), IRanges, Rsamtools (>= 1.17.8),

+        rtracklayer (>= 1.31.2), GenomicFeatures (>= 1.17.13), Biostrings,

+        VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,

+        GenomicAlignments (>= 1.1.9), BiocParallel

 Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,

         BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,

         TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,

@@ -31,7 +31,7 @@ setReplaceMethod("snps", c("GmapSnpDirectory", "character", "VCF"),

                    iitFile <- file.path(iitPath, paste(name, "iit", sep = "."))

                    alt <- values(gr)$ALT

                    if (is(alt, "List")) {

-                     gr <- rep(gr, elementLengths(alt))

+                     gr <- rep(gr, elementNROWS(alt))

                      alt <- unlist(alt)

                    }

                    ref <- values(gr)$REF