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

 Package: bsseq

-Version: 1.1.1

+Version: 1.1.2

 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"),

@@ -7,6 +7,8 @@ setValidity("BSseq", function(object) {

     if(class(rowData(object)) != "GRanges")

         msg <- validMsg(msg, sprintf("object of class '%s' needs to have a 'GRanges' in slot 'rowData'", class(object)))

     ## benchmarking shows that min(assay()) < 0 is faster than any(assay() < 0) if it is false

+    if(is.null(colnames(object)))

+        msg <- validMsg(msg, "colnames (aka sampleNames) need to be set")

     if(min(assay(object, "M")) < 0)

         msg <- validMsg(msg, "the 'M' assay has negative entries")

     if(min(assay(object, "Cov")) < 0)

@@ -1,16 +1,13 @@

 bibentry("Article",

          title = "{BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions}",

-         author = personList(

-         person(c("Kasper", "D."), "Hansen"),

-         person("Benjamin", "Langmead"),

-         person(c("Rafael", "A."), "Irizarry")),

+         author = "Hansen, Kasper D. and Langmead, Benjamin and Irizarry, Rafael A.",

          journal = "Genome Biology",

-         year = 2012,

+         year = "2012",

 	 volume = "13",

 	 pages = "R83",

   	 textVersion = 

-         paste("KD Hansen, B Langmead, and RA Irizarry.",

+         paste("KD Hansen, B Langmead and RA Irizarry.",

                "BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.", 

-"Genome Biology, 13:R83 (2012)")

+               "Genome Biology, 13:R83 (2012)")

 )

@@ -21,6 +21,11 @@

     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>.

+    \item validity now checks for the presence of colnames (sampleNames)

+    which was assumed to be set.  Reported by Kevin Rue-Albrecht

+    <kevin.rue@ucdconnect.ie>.

+    \item Fixed a man page issue.

+    \item SLightly changed CITATION.

   }

 }

@@ -18,6 +18,7 @@

 \alias{start<-,hasGRanges-method}

 \alias{strand,hasGRanges-method}

 \alias{strand<-,hasGRanges-method}

+\alias{strand<-,hasGRanges,ANY-method}

 \alias{subsetByOverlaps,GenomicRanges,hasGRanges-method}

 \alias{subsetByOverlaps,hasGRanges,GenomicRanges-method}

 \alias{subsetByOverlaps,hasGRanges,hasGRanges-method}