@@ -1,5 +1,5 @@

 Package: bsseq

-Version: 0.11.4

+Version: 0.11.5

 Title: Analyze, manage and store bisulfite sequencing data

 Description: Tools for analyzing and visualizing bisulfite sequencing data

 Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),

@@ -72,7 +72,7 @@ combineList <- function(x, ...) {

     if(!all(sameTrans))

         stop("all elements of '...' in combineList needs to have the same trans")

     sameGr <- sapply(x[-1], function(xx) {

-        identical(trans, getBSseq(xx, "gr"))

+        identical(gr, getBSseq(xx, "gr"))

     })

     if(all(sameGr)) {

         M <- do.call(cbind, lapply(x, function(xx) getBSseq(xx, "M")))

@@ -15,7 +15,12 @@

     <jroux@uchicago.edu>: it would use the Meth values instead of Cov

     for the final object's Cov.  However, this will result in the return

     object having a methylation of 100 percent across all loci, so

-    hopefully users will have seen this for themselves. 

+    hopefully users will have seen this for themselves.

+    \item Fixed a bug in combineList which made combineList use "slow"

+    code even in a special case where a faster shortcut was possible.

+    This bug fix does not change the output of the function under any

+    input, it only makes it faster.  Reported by Julien Roux

+    <jroux@uchicago.edu>.

   }

 }