@@ -9,10 +9,10 @@ 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: 1.21.1

+Version: 1.21.2

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

         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)

-Imports: S4Vectors (>= 0.13.13), IRanges, 

+Imports: S4Vectors (>= 0.13.13), IRanges, BiocGenerics (>= 0.25.1),

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

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

         GenomicAlignments (>= 1.1.9), BiocParallel

@@ -1,6 +1,7 @@

 useDynLib(gmapR, .registration = TRUE)

-importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,

+importFrom(BiocGenerics, path)

+importFrom(Rsamtools, bamPaths, "bamWhich<-", BamFile, BamFileList,

            BamSampler)

 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,

            list_files_with_exts)

@@ -12,7 +13,8 @@ import(GenomicRanges)

 import(GenomeInfoDb)

 import(BiocParallel)

 importMethodsFrom(GenomeInfoDb, genome)

-importFrom(utils, packageVersion)

+importFrom(stats, setNames)

+importFrom(utils, packageVersion, read.table, str)

 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)

 importMethodsFrom(GenomicRanges, seqnames, strand)

 importMethodsFrom(Rsamtools, asBam)