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Don't use 'order.as.in.query=TRUE' (defunct in BioC 3.3) when calling grglist() on a GAlignmentPairs object.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@110191 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 02/11/2015 06:55:12
Showing 3 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: 1.11.0
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+Version: 1.11.1
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 Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages
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 License: Artistic-2.0
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 Description: This package allows the user to create, manipulate, and visualize
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@@ -88,8 +88,10 @@ assignReads <- function(sg, reads, sample.name=NA)
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 {
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     if (!is(sg, "SplicingGraphs"))
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         stop("'sg' must be a SplicingGraphs object")
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-    if (is(reads, "GAlignments") || is(reads, "GAlignmentPairs")) {
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+    if (is(reads, "GAlignments")) {
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         reads <- grglist(reads, order.as.in.query=TRUE)
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+    } else if (is(reads, "GAlignmentPairs")) {
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+        reads <- grglist(reads)
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     } else if (!is(reads, "GRangesList")) {
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         stop("'reads' must be a GAlignments, GAlignmentPairs, ",
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              "or GRangesList object")
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@@ -113,7 +113,11 @@
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             idx <- order(sample(reads_len, max.plot.reads))
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             reads <- reads[idx]
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         }
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-        grl <- grglist(reads, order.as.in.query=TRUE)
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+        if (is(reads, "GAlignments")) {
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+            grl <- grglist(reads, order.as.in.query=TRUE)
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+        } else {
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+            grl <- grglist(reads)
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+        }
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         ov0 <- findOverlaps(grl, x, ignore.strand=TRUE)
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         ovenc0 <- encodeOverlaps(grl, x, hits=ov0,
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                                  flip.query.if.wrong.strand=TRUE)