@@ -10,14 +10,11 @@ Description: This package allows the user to create, manipulate, and visualize

 	the edges of a set of splicing graphs, and to summarize them in

         different ways.

 Maintainer: H. Pages <[email protected]>

-Depends: BiocGenerics,

-	 S4Vectors (>= 0.5.16), IRanges (>= 1.99.21),

-	 GenomicRanges (>= 1.17.22), GenomicFeatures (>= 1.17.13),

-	 GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7)

+Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22),

+	 Rgraphviz (>= 2.3.7)

 Imports: methods, utils, igraph,

-	 BiocGenerics,

-	 IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments,

-	 graph, Rgraphviz

+	 BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,

+	 GenomicFeatures, GenomicAlignments, graph, Rgraphviz

 Suggests: igraph, Gviz, Rsamtools (>= 1.19.17),

 	 TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14,

 	 RUnit

@@ -8,14 +8,15 @@ importFrom(igraph, graph.data.frame, get.data.frame, layout.kamada.kawai,

 import(BiocGenerics)

 import(S4Vectors)

 import(IRanges)

+import(GenomeInfoDb)

 import(GenomicRanges)

 import(GenomicFeatures)

 import(GenomicAlignments)

 importFrom(graph, nodeDataDefaults, nodeData,

-                  edgeDataDefaults, edgeNames, edgeData)

+                  edgeDataDefaults, edgeNames, edgeData, edgemode)

-importFrom(Rgraphviz, agopen)

+importFrom(Rgraphviz, agopen, buildEdgeList, buildNodeList, from, to)

 exportClasses(GeneModel, SplicingGraphs)

@@ -18,6 +18,10 @@ toy_reads_sam <- function()

 toy_reads_bam <- function()

 {

+    ## The Rsamtools package is needed for asBam().

+    if (!requireNamespace("Rsamtools", quietly=TRUE))

+        stop("Couldn't load the Rsamtools package. Please install ",

+             "the Rsamtools\n  package and try again.")

     toy_reads_bam <- try(get("toy_reads_bam", envir=.toy_reads_bam_cache,

                              inherits=FALSE), silent=TRUE)

     if (!is(toy_reads_bam, "try-error"))

@@ -65,7 +65,7 @@ make_TSPC_SplicinGraphs <- function(subdir_paths)

         })

     suppressWarnings(ex_by_tx <- do.call(c, unname(gene_list)))

     ex_by_tx_seqlevels <- seqlevels(ex_by_tx)

-    seq_rank <- makeSeqnameIds(ex_by_tx_seqlevels)

+    seq_rank <- rankSeqlevels(ex_by_tx_seqlevels)

     seqlevels(ex_by_tx) <- ex_by_tx_seqlevels[order(seq_rank)]

     grouping <- rep.int(basename(subdir_paths), elementLengths(gene_list))

     SplicingGraphs(ex_by_tx, grouping=grouping, min.ntx=1L)