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

 Package: SplicingGraphs

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

 	to them

-Version: 1.11.0

+Version: 1.11.1

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

 License: Artistic-2.0

 Description: This package allows the user to create, manipulate, and visualize

@@ -88,8 +88,10 @@ assignReads <- function(sg, reads, sample.name=NA)

 {

     if (!is(sg, "SplicingGraphs"))

         stop("'sg' must be a SplicingGraphs object")

-    if (is(reads, "GAlignments") || is(reads, "GAlignmentPairs")) {

+    if (is(reads, "GAlignments")) {

         reads <- grglist(reads, order.as.in.query=TRUE)

+    } else if (is(reads, "GAlignmentPairs")) {

+        reads <- grglist(reads)

     } else if (!is(reads, "GRangesList")) {

         stop("'reads' must be a GAlignments, GAlignmentPairs, ",

              "or GRangesList object")

@@ -113,7 +113,11 @@

             idx <- order(sample(reads_len, max.plot.reads))

             reads <- reads[idx]

         }

-        grl <- grglist(reads, order.as.in.query=TRUE)

+        if (is(reads, "GAlignments")) {

+            grl <- grglist(reads, order.as.in.query=TRUE)

+        } else {

+            grl <- grglist(reads)

+        }

         ov0 <- findOverlaps(grl, x, ignore.strand=TRUE)

         ovenc0 <- encodeOverlaps(grl, x, hits=ov0,

                                  flip.query.if.wrong.strand=TRUE)