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made combineList faster by fixing a typo

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@86674 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 21/02/2014 14:46:59
Showing3 changed files

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@@ -1,5 +1,5 @@
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 Package: bsseq
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-Version: 0.11.4
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+Version: 0.11.5
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 Title: Analyze, manage and store bisulfite sequencing data
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 Description: Tools for analyzing and visualizing bisulfite sequencing data
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 Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
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@@ -72,7 +72,7 @@ combineList <- function(x, ...) {
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     if(!all(sameTrans))
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         stop("all elements of '...' in combineList needs to have the same trans")
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     sameGr <- sapply(x[-1], function(xx) {
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-        identical(trans, getBSseq(xx, "gr"))
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+        identical(gr, getBSseq(xx, "gr"))
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     })
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     if(all(sameGr)) {
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         M <- do.call(cbind, lapply(x, function(xx) getBSseq(xx, "M")))
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@@ -15,7 +15,12 @@
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     <jroux@uchicago.edu>: it would use the Meth values instead of Cov
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     for the final object's Cov.  However, this will result in the return
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     object having a methylation of 100 percent across all loci, so
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-    hopefully users will have seen this for themselves. 
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+    hopefully users will have seen this for themselves.
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+    \item Fixed a bug in combineList which made combineList use "slow"
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+    code even in a special case where a faster shortcut was possible.
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+    This bug fix does not change the output of the function under any
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+    input, it only makes it faster.  Reported by Julien Roux
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+    <jroux@uchicago.edu>.
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   }
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 }
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