@@ -10,11 +10,11 @@ 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: 1.7.5

+Version: 1.7.6

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

         GenomicRanges (>= 1.17.12)

 Imports: S4Vectors, IRanges, Rsamtools (>= 1.17.8), rtracklayer (>= 1.25.5),

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

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

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

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

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

@@ -14,7 +14,7 @@ import(GenomeInfoDb)

 import(GenomicRanges)

 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)

 importMethodsFrom(Rsamtools, asBam)

-importClassesFrom(GenomicFeatures, TranscriptDb)

+importClassesFrom(GenomicFeatures, TxDb)

 importFrom(GenomicFeatures, transcripts, exons)

 importClassesFrom(rtracklayer, RTLFile, FastaFile)

 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)

@@ -154,7 +154,7 @@ setReplaceMethod("spliceSites", c("GmapGenome", "GRangesList"),

                    x

                  })

-setReplaceMethod("spliceSites", c("GmapGenome", "TranscriptDb"),

+setReplaceMethod("spliceSites", c("GmapGenome", "TxDb"),

                  function(x, name, value) {

                    spliceSites(x, name) <- exonsBy(value)

                    x

@@ -9,7 +9,7 @@

 \alias{GmapGenome}

 \alias{snps<-,GmapGenome,ANY,ANY-method}

 \alias{spliceSites<-,GmapGenome,GRangesList-method}

-\alias{spliceSites<-,GmapGenome,TranscriptDb-method}

+\alias{spliceSites<-,GmapGenome,TxDb-method}

 \alias{coerce,GmapGenome,DNAStringSet-method}

 \alias{snps<-}

 \alias{spliceSites<-}