Return empty objects when receiving empty objects.

Closes #25

R/Translocations.R

@@ -46,6 +46,10 @@
 #' @export
 
 flagTranslocations <- function (gb, tol = Inf, both = TRUE) {
+  if(length(gb) == 0) {
+    gb$tra <- Rle(logical(0))
+    return(gb)
+  }
   # Enforce sorting, to guarantee colinearity on the _target_ranges
   if (isFALSE(isSorted(gb))) stop ("Can not run on non-sorted objects.")
   gb.bak <- gb # save the original object

R/flagColinearAlignments.R

@@ -83,7 +83,10 @@ flagColinearAlignments <- function(gb, tol = Inf, minwidth = 0, details = FALSE)
   gb <- gb[width(gb$query) >= minwidth]
 
   # Handle empty objects
-  if (length(gb) == 0) return(gb)
+  if(length(gb) == 0) {
+    gb$colinear <- logical(0)
+    return(gb)
+  }
 
   # Sort the ranges following the target genome.  The argument
   # ignore.strand = TRUE is set so that alignments on the opposite strand can

R/flagInversions.R

@@ -37,6 +37,10 @@
 #' @export
 
 flagInversions <- function (gb, tol = Inf) {
+  if(length(gb) == 0) {
+    gb$inv <- Rle(logical(0))
+    return(gb)
+  }
   if (isFALSE(isSorted(gb))) stop ("Can not run on non-sorted objects.")
   gb.bak <- gb # save the original object
   gb <- dist2next(gb, ignore.strand = TRUE)
@@ -113,6 +117,10 @@ flagInversions <- function (gb, tol = Inf) {
 #' @export
 
 flagDoubleInversions <- function(gb, details = FALSE) {
+  if(length(gb) == 0) {
+    gb$Dbl <- Rle(logical(0))
+    return(gb)
+  }
   if (isFALSE(isSorted(gb))) stop ("Can not run on non-sorted objects.")
 
   gb.bak <- gb # Backup the object
@@ -194,6 +202,7 @@ flagDoubleInversions <- function(gb, details = FALSE) {
 #' @export
 
 showInversions <- function(gb, rename = TRUE) {
+  if(length(gb) == 0) return(gb)
   if (is.null(gb$inv)) return(gb[0])
   if (isTRUE(rename))
     names(gb) <- seq_along(gb)

R/flagPairs.R

@@ -70,6 +70,10 @@ allPossiblePairClasses <- with(allPossiblePairClasses, {
 #' @export
 
 flagPairs <- function (gb) {
+  if(length(gb) == 0) {
+    gb$pairs <- factor(character(0))
+    return(gb)
+  }
   if (isFALSE(isSorted(gb))) stop ("Can not run on non-sorted objects.")
   gb.bak <- gb # save the original object