diff -Nru r-bioc-shortread-1.34.2/debian/changelog r-bioc-shortread-1.36.0/debian/changelog
--- r-bioc-shortread-1.34.2/debian/changelog	2017-10-22 17:30:51.000000000 +0000
+++ r-bioc-shortread-1.36.0/debian/changelog	2017-11-09 07:46:50.000000000 +0000
@@ -1,3 +1,9 @@
+r-bioc-shortread (1.36.0-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Andreas Tille <tille@debian.org>  Thu, 09 Nov 2017 08:46:50 +0100
+
 r-bioc-shortread (1.34.2-1) unstable; urgency=medium
 
   * New upstream version
diff -Nru r-bioc-shortread-1.34.2/DESCRIPTION r-bioc-shortread-1.36.0/DESCRIPTION
--- r-bioc-shortread-1.34.2/DESCRIPTION	2017-10-07 22:41:16.000000000 +0000
+++ r-bioc-shortread-1.36.0/DESCRIPTION	2017-10-30 22:51:24.000000000 +0000
@@ -1,7 +1,7 @@
 Package: ShortRead
 Type: Package
 Title: FASTQ input and manipulation
-Version: 1.34.2
+Version: 1.36.0
 Author: Martin Morgan, Michael Lawrence, Simon Anders
 Maintainer: Bioconductor Package Maintainer
  <maintainer@bioconductor.org>
@@ -14,7 +14,7 @@
         alignment formats.
 License: Artistic-2.0
 LazyLoad: yes
-Depends: BiocGenerics (>= 0.22.1), BiocParallel, Biostrings (>=
+Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>=
         2.37.1), Rsamtools (>= 1.21.4), GenomicAlignments (>= 1.5.4)
 Imports: Biobase, S4Vectors (>= 0.13.8), IRanges (>= 2.3.7),
         GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.21.6), hwriter,
@@ -23,4 +23,4 @@
 LinkingTo: S4Vectors, IRanges, XVector, Biostrings
 biocViews: DataImport, Sequencing, QualityControl
 NeedsCompilation: yes
-Packaged: 2017-10-07 22:41:16 UTC; biocbuild
+Packaged: 2017-10-30 22:51:24 UTC; biocbuild
Binary files /tmp/tmpv64Nst/NkvaGsO6E6/r-bioc-shortread-1.34.2/inst/doc/Overview.pdf and /tmp/tmpv64Nst/szznNjZhm_/r-bioc-shortread-1.36.0/inst/doc/Overview.pdf differ
diff -Nru r-bioc-shortread-1.34.2/man/Snapshot-class.Rd r-bioc-shortread-1.36.0/man/Snapshot-class.Rd
--- r-bioc-shortread-1.34.2/man/Snapshot-class.Rd	2017-08-30 21:21:28.000000000 +0000
+++ r-bioc-shortread-1.36.0/man/Snapshot-class.Rd	2017-10-30 21:20:26.000000000 +0000
@@ -235,7 +235,7 @@
 
 getAnnGR <- function(txdb, which) {
     ex <- exonsBy(txdb, by="gene")
-    seqlevels(ex, force=TRUE) <- seqlevels(which)
+    seqlevels(ex, pruning.mode="coarse") <- seqlevels(which)
     r <- range(ex)
     gr <- unlist(r)
     values(gr)[["gene_id"]] <- rep.int(names(r), times=lengths(r))
diff -Nru r-bioc-shortread-1.34.2/R/SnapshotFunction-helpers.R r-bioc-shortread-1.36.0/R/SnapshotFunction-helpers.R
--- r-bioc-shortread-1.34.2/R/SnapshotFunction-helpers.R	2017-08-30 21:21:27.000000000 +0000
+++ r-bioc-shortread-1.36.0/R/SnapshotFunction-helpers.R	2017-10-30 21:20:26.000000000 +0000
@@ -183,7 +183,7 @@
     ignore.strand <- ignore.strand(x)
     if (any(seqnames(anntrack)@values %in% seqlevels(rng))) {
         gr <- anntrack
-        seqlevels(gr, force=TRUE) <- seqlevels(vrange(x))
+        seqlevels(gr, pruning.mode="coarse") <- seqlevels(vrange(x))
     } else  {
         message(paste(strwrap("SnapshotFunction-helper: seqname of
            'annTrack' does not match the imported range. Annotation
diff -Nru r-bioc-shortread-1.34.2/R/spViewPerFeature.R r-bioc-shortread-1.36.0/R/spViewPerFeature.R
--- r-bioc-shortread-1.34.2/R/spViewPerFeature.R	2017-08-30 21:21:27.000000000 +0000
+++ r-bioc-shortread-1.36.0/R/spViewPerFeature.R	2017-10-30 21:20:26.000000000 +0000
@@ -28,7 +28,7 @@
         stop(sprintf("element named '%s' does not exist", name))
     
     gr <- GRL[[name]]
-    seqlevels(gr, force=TRUE) <- levels(seqnames(gr))
+    seqlevels(gr, pruning.mode="coarse") <- levels(seqnames(gr))
     which <- reduce(range(gr))
     annTrack <- gr