On Tue, Aug 7, 2012 at 12:11 AM, Lescai,
    Francesco<f.lescai@ucl.ac.uk <mailto:f.lescai@ucl.ac.uk>>wrote:

        Hi there,
        I'm having an error in exomeCopy when I count the CNVs.
        No previous error in any of the other steps illustrated in the
        vignette

        the computation of the fit list didn't give any warning and it
        seems to be formatted correctly

         > fit.list[[1]][1]
        $`1`

        ExomeCopy object
        sample name: UCLG_502_ATCACG_L003
        percent normal state: 79.87%

         > summary(fit.list$UCLG_502_ATCACG_L003$`1`)
            Length     Class      Mode
                 1 ExomeCopy        S4

        but then I get

         > compiled.segments <- compileCopyCountSegments(fit.list)
        Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE =
        "IRanges") :
           solving row 1: negative widths are not allowed



Hi Francesco,

I have seen this error before when the target GRanges has duplicate or 
unsorted regions, and fixed this in the devel branch.  You could try to 
reduce the target GRanges first, before counting sample read counts.  
Could you try:

all.equal(target, reduce(target))

If these are in fact equal, you can send me the fit.list object and I 
can try to debug.

best,

Mike

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