git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs@110191 bc3139a8-67e5-0310-9ffc-ced21a209358
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@@ -1,7 +1,7 @@ |
1 | 1 |
Package: SplicingGraphs |
2 | 2 |
Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads |
3 | 3 |
to them |
4 |
-Version: 1.11.0 |
|
4 |
+Version: 1.11.1 |
|
5 | 5 |
Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages |
6 | 6 |
License: Artistic-2.0 |
7 | 7 |
Description: This package allows the user to create, manipulate, and visualize |
... | ... |
@@ -88,8 +88,10 @@ assignReads <- function(sg, reads, sample.name=NA) |
88 | 88 |
{ |
89 | 89 |
if (!is(sg, "SplicingGraphs")) |
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stop("'sg' must be a SplicingGraphs object") |
91 |
- if (is(reads, "GAlignments") || is(reads, "GAlignmentPairs")) { |
|
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+ if (is(reads, "GAlignments")) { |
|
92 | 92 |
reads <- grglist(reads, order.as.in.query=TRUE) |
93 |
+ } else if (is(reads, "GAlignmentPairs")) { |
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+ reads <- grglist(reads) |
|
93 | 95 |
} else if (!is(reads, "GRangesList")) { |
94 | 96 |
stop("'reads' must be a GAlignments, GAlignmentPairs, ", |
95 | 97 |
"or GRangesList object") |
... | ... |
@@ -113,7 +113,11 @@ |
113 | 113 |
idx <- order(sample(reads_len, max.plot.reads)) |
114 | 114 |
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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+ } |
|
117 | 121 |
ov0 <- findOverlaps(grl, x, ignore.strand=TRUE) |
118 | 122 |
ovenc0 <- encodeOverlaps(grl, x, hits=ov0, |
119 | 123 |
flip.query.if.wrong.strand=TRUE) |