@@ -1,5 +1,5 @@

 Package: bsseq

-Version: 1.11.3-1

+Version: 1.13.3

 Encoding: UTF-8

 Title: Analyze, manage and store bisulfite sequencing data

 Description: A collection of tools for analyzing and visualizing bisulfite

@@ -41,7 +41,7 @@ collapseBSseq <- function(BSseq, columns) {

 }

 chrSelectBSseq <- function(BSseq, seqnames = NULL, order = FALSE) {

-    seqlevels(BSseq, force = TRUE) <- seqnames

+    seqlevels(BSseq, pruning.mode = "coarse") <- seqnames

     if(order)

         BSseq <- orderBSseq(BSseq, seqOrder = seqnames)

     BSseq

@@ -50,7 +50,7 @@ chrSelectBSseq <- function(BSseq, seqnames = NULL, order = FALSE) {

 orderBSseq <- function(BSseq, seqOrder = NULL) {

     if(!is.null(seqOrder))

-        seqlevels(BSseq, force = TRUE) <- seqOrder

+        seqlevels(BSseq, pruning.mode = "coarse") <- seqOrder

     BSseq[order(granges(BSseq))]

 }

Binary files a/data/BS.chr22.rda and b/data/BS.chr22.rda differ