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

 Package: SplicingGraphs

 Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads

 	to them

-Version: 1.17.0

+Version: 1.17.1

 Encoding: UTF-8

 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pagès

 License: Artistic-2.0

@@ -19,9 +19,9 @@

     ## Drop all sequence levels but the one level that is used by the single

     ## range in 'subject'.

     seqlevels(subject) <- as.character(seqnames(subject))

-    ## Set the same one sequence level on 'query'. Use 'force=TRUE' to remove

-    ## the elements in 'query' that are not on that sequence level.

-    seqlevels(query, force=TRUE) <- seqlevels(subject)

+    ## Set the same one sequence level on 'query'. Use 'pruning.mode="coarse"'

+    ## to remove the elements in 'query' that are not on that sequence level.

+    seqlevels(query, pruning.mode="coarse") <- seqlevels(subject)

     query_ranges <- granges(query)

     strand(query_ranges) <- "*"