@@ -1,6 +1,6 @@

 Package: CNEr 

-Version: 1.9.40

-Date: 2016-09-20

+Version: 1.9.41

+Date: 2016-10-04

 Title: CNE Detection and Visualization

 Description: Large-scale identification and advanced visualization 

              of sets of conserved noncoding elements.

@@ -42,6 +42,7 @@ readAncora <- function(fn, assembly=NULL,

                                    name=paste0(cne[[4]], ":", 

                                                (cne[[5]]+1), "-", cne[[6]]),

                                    itemRgb=chr2colour(cne[[4]]),

+                                   seqnames2=cne[[4]],

                                    seqinfo=seqinfoTarget),

                      second=GRanges(seqnames=cne[[4]],

                                   ranges=IRanges(start=cne[[5]]+1,

@@ -49,6 +50,7 @@ readAncora <- function(fn, assembly=NULL,

                                   strand="*",

                                   name=paste0(cne[[1]], ":", 

                                               (cne[[2]]+1), "-", cne[[3]]),

+                                  seqnames2=cne[[1]],

                                   itemRgb=chr2colour(cne[[1]]),

                                   seqinfo=seqinfoQuery)

                      )

@@ -2,11 +2,19 @@

 ### make GRBs from CNEs

 ### Exported!

 makeGRBs <- function(x, winSize=NULL, genes=NULL, ratio=1, 

-                     background=c("chromosome", "genome")){

+                     background=c("chromosome", "genome")){#,

+                     #byChrom=FALSE

   if(!is(x, "GRangesList")){

     stop("The input `x` must be a `GRangesList` object!")

   }

   background <- match.arg(background)

+  # if(isTRUE(byChrom)){

+  #   if(!all(sapply(cneList, 

+  #                  function(x){"seqnames2" %in% colnames(mcols(x))}))){

+  #     stop("`x` must have metacolum of `seqnames2` to do",

+  #          "byChrom GRB prediction!")

+  #   }

+  # }

   xList <- x

   if(is.null(names(xList))){

@@ -283,6 +283,12 @@ readCNERangesFromSQLite <- function(dbName, tableName,

     seqinfoQuery <- seqinfoFn(qAssemblyFn)

   }

+  # Return empty GRangePairs when no CNEs are returned.

+  if(nrow(fetchedCNE) == 0L){

+    return(GRangePairs(first=GRanges(seqinfo=seqinfoTarget),

+                       second=GRanges(seqinfo=seqinfoQuery)))

+  }

+  

   firstGRanges <- GRanges(seqnames=fetchedCNE[ ,1],

                           ranges=IRanges(start=fetchedCNE[ ,2],

                                          end=fetchedCNE[,3]),