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

 Package: CNEr 

-Version: 1.9.38

-Date: 2016-08-25

+Version: 1.9.39

+Date: 2016-09-12

 Title: CNE Detection and Visualization

 Description: Large-scale identification and advanced visualization 

              of sets of conserved noncoding elements.

@@ -46,7 +46,7 @@ importFrom(S4Vectors, .Call2, queryHits, subjectHits, DataFrame,

            isTRUEorFALSE, isSingleString, queryLength, subjectLength)

 importFrom(tools, file_ext)

 importFrom(parallel, mcmapply)

-importFrom(utils, download.file, read.table, write.table)

+importFrom(utils, download.file, read.table, write.table, read.delim)

 importFrom("stats", "setNames")

 importFrom(reshape2, melt)

 importFrom(ggplot2, ggplot, aes, aes_q, aes_string, geom_tile, theme_bw, 

@@ -23,7 +23,7 @@ readAncora <- function(fn, assembly=NULL,

                        tAssemblyFn=NULL, qAssemblyFn=NULL){

   assembly1 <- strsplit(basename(fn), split="_")[[1]][2]

   assembly2 <- strsplit(basename(fn), split="_")[[1]][3]

-  cne <- suppressMessages(read_tsv(fn, col_names=FALSE))

+  cne <- read.delim(fn, header=FALSE)

   # Prepare the seqinfo when available

   seqinfoTarget <- NULL

@@ -35,21 +35,21 @@ readAncora <- function(fn, assembly=NULL,

     seqinfoQuery <- seqinfoFn(qAssemblyFn)

   }

-  ans <- GRangePairs(first=GRanges(seqnames=cne$X1,

-                                   ranges=IRanges(start=cne$X2+1,

-                                                  end=cne$X3),

+  ans <- GRangePairs(first=GRanges(seqnames=cne[[1]],

+                                   ranges=IRanges(start=cne[[2]]+1,

+                                                  end=cne[[3]]),

                                    strand="*",

-                                   name=paste0(cne$X4, ":", 

-                                               (cne$X5+1), "-", cne$X6),

-                                   itemRgb=chr2colour(cne$X4),

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

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

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

                                    seqinfo=seqinfoTarget),

-                     second=GRanges(seqnames=cne$X4,

-                                  ranges=IRanges(start=cne$X5+1,

-                                                 end=cne$X6),

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

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

+                                                 end=cne[[6]]),

                                   strand="*",

-                                  name=paste0(cne$X1, ":", 

-                                              (cne$X2+1), "-", cne$X3),

-                                  itemRgb=chr2colour(cne$X1),

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

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

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

                                   seqinfo=seqinfoQuery)

                      )

   if(is.null(assembly)){

@@ -73,7 +73,13 @@ ceScanR <- function(axts, tFilter=NULL, qFilter=NULL, tSizes, qSizes,

   }

   CNE <- lapply(resFiles, 

                 function(x){

-                  res <- read.table(x, header=FALSE, sep="\t", as.is=TRUE)

+                  res <- try(read.table(x, header=FALSE, sep="\t", as.is=TRUE),

+                             silent=TRUE)

+                  if(class(res) == "try-error"){

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

+                                       second=GRanges(seqinfo=qSizes))

+                           )

+                  }

                   colnames(res) <- c("tName", "tStart", "tEnd", 

                                      "qName", "qStart", "qEnd",

                                      "strand", "score", "cigar")