Hi, 

I have multiple IRanges separated by certain distance which I would like
to merge by REDUCE with the parameter min.gapwidth. If an IRange is
within the min.gapwidth, but the coverage is too low, say, only 1 or 2
across, I'd like to skip it, ie,  do not perform REDUCE. Could anyone
suggest a good way to do it? Thanks.

-Kunbin

Example like the following: 

> x<-IRanges(c(1,1,2,3,3,7,10,10,11), c(2,3,3,4,5,8,11,12,13))
> x
IRanges of length 9
    start end width
[1]     1   2     2
[2]     1   3     3
[3]     2   3     2
[4]     3   4     2
[5]     3   5     3
[6]     7   8     2
[7]    10  11     2
[8]    10  12     3
[9]    11  13     3
> coverage(x)
'integer' Rle of length 13 with 12 runs
  Lengths: 1 1 1 1 1 1 2 1 1 1 1 1
  Values : 2 3 4 2 1 0 1 0 2 3 2 1
> xr<-reduce(x, min.gapwidth=2)
> xr
IRanges of length 1
    start end width
[1]     1  13    13

IRange No. 6 is the weak link with a coverage of 1 in the middle, but it
links IRanges 1 to 5 with IRanges 7 to 9 to cause only one IRange after
REDUCE. 

I'd like to avoid this, so REDUCE will result two clusters, one from
IRanges 1 to 5, another from IRanges 7 to 9. 


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