cleanGaps: support colinear GBreaks objects and zero-width ranges.

[charles-plessy]

Some GBreak objects contain adjacent ranges, that return nothing when passed through cleanGaps.

> gr <- GRanges(c("a:1-10:+", "a:11-20:+"))
> gr
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]        a      1-10      +
  [2]        a     11-20      +
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> cleanGaps(gr)
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

The function needs to be modified so that it returns a zero-width range. Here is an idea:

> cleanGaps(gr - 1)
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]        a     10-11      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> cleanGaps(gr - 1) -1
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]        a     11-10      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> width(cleanGaps(gr - 1) -1)
[1] 0

Once this is done, it should be possible to pass a GBreaks object containing only colinear ranges, and to turn it into colinear double-gap regions.