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

 Package: bsseq

-Version: 0.11.3

+Version: 0.11.4

 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"),

@@ -14,7 +14,7 @@ collapseBSseq <- function(BSseq, columns) {

         rowSums(getBSseq(BSseq, "M")[, ss, drop = FALSE])

     }))

     Cov <- do.call(cbind, lapply(sp, function(ss) {

-        rowSums(getBSseq(BSseq, "M")[, ss, drop = FALSE])

+        rowSums(getBSseq(BSseq, "Cov")[, ss, drop = FALSE])

     }))

     BSseq(gr = getBSseq(BSseq, "gr"), M = M, Cov = Cov, sampleNames = names(sp))

 }

@@ -11,6 +11,11 @@

     \item Fixed an issue introduced by the previous change (to

     plotRegion).  Reported (with a fix) by Tim Triche Jr

     <tim.triche@gmail.com>.

+    \item Fixed a serious bug in collapseBSseq reported by Julien Roux

+    <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. 

   }

 }