Hello,

I am getting an error while trying to use a function to count reads for every chromosome across the genome in bins of 50bp (windowAnalysis function from groHMM package). The error is only for one chromosome and runs fine for rest of the chromosomes. Upon reading, I found that it is related to IRanges package. Following is the error: 

$chrM

1] "Error in normalizeDoubleBracketSubscript(i, x, exact = exact, error.if.nomatch = FALSE) : \n  subscript is out of bounds\n"

attr(,"class")

[1] "try-error"

attr(,"condition")

<simpleError in normalizeDoubleBracketSubscript(i, x, exact = exact, error.if.nomatch = FALSE): subscript is out of bounds>

Example for how it works fine for other chromosomes:

$chr1

integer-Rle of length 4985012 with 64 runs

  Lengths: 935331      1      1 478754      1 ... 228032      1      1   1650

  Values :      0     47      4      0      1 ...      0      1     50      0

Any suggestions to fix this is greatly appreciated.

Thanks,

Anusha