Browse code

Fix various issues

These issues were caused by changes in the S4Vectors, IRanges, and
GenomicRanges packages that happened over the last 3 months.

Hervé Pagès authored on 26/04/2018 07:21:39
Showing 4 changed files

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@@ -1,7 +1,7 @@
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 Package: SplicingGraphs
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 Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads
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 	to them
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-Version: 1.19.1
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+Version: 1.19.2
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 Encoding: UTF-8
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 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pagès
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 License: Artistic-2.0
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@@ -210,7 +210,7 @@ setMethod("[", "SplicingGraphs",
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         seqx <- seq_along(x_genes)
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         names(seqx) <- names(x_genes)
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         i <- seqx[i]
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-        ii <- unlist(IRanges(PartitioningByEnd(x_genes))[i], use.names=FALSE)
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+        ii <- IRanges:::unlist_as_integer(IRanges(PartitioningByEnd(x_genes))[i])
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         x@genes <- x_genes[i]
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         x@in_by_tx <- x@in_by_tx[ii]
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         x
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@@ -501,6 +501,7 @@ setMethod("show", "SplicingGraphs",
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 {
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     if (!is(x, "GRangesList"))
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         stop("'x' must be a GRangesList object")
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+    metadata(x) <- list()
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     if (is.null(grouping)) {
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         if (!identical(min.ntx, 2) || !identical(max.ntx, NA))
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             stop("the 'min.ntx' and 'max.ntx' args are not supported ",
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Binary files a/vignettes/precomputed_results/sg_with_bubbles.rda and b/vignettes/precomputed_results/sg_with_bubbles.rda differ
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Binary files a/vignettes/precomputed_results/sg_with_reads.rda and b/vignettes/precomputed_results/sg_with_reads.rda differ