Hi Jesper,

Would you be willing to volunteer your use case? As Herve hinted,
cigarToRleList and friends are low-level helpers. There may be an easier
way to achieve what you want, or an opportunity to improve things.

Michael


On Mon, Feb 17, 2014 at 1:10 AM, Jesper Gådin <jesper.gadin@gmail.com>wrote:

> Hi,
>
> Have come across a cigar-vector that is problematic to process.
>
> #load package
> > library(GenomicAlignments)
>
> #load data (see attached file)
> > load("2014-02-17-cigarExample.rdata")
>
> #run function cigarToRleList
> > cigarRle <- cigarToRleList(cigarExample)
> Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE =
> "IRanges") :
>   integer overflow while summing elements in 'lengths'
>
> > sessionInfo()
> R Under development (unstable) (2013-11-13 r64209)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] GenomicAlignments_0.99.18 Rsamtools_1.15.26
> [3] Biostrings_2.31.12        XVector_0.3.6
> [5] GenomicRanges_1.15.26     IRanges_1.21.23
> [7] BiocGenerics_0.9.3
>
> loaded via a namespace (and not attached):
>  [1] BatchJobs_1.1-1135 BBmisc_1.5         BiocParallel_0.5.8 bitops_1.0-6
>
>  [5] brew_1.0-6         codetools_0.2-8    DBI_0.2-7          digest_0.6.4
>
>  [9] fail_1.2           foreach_1.4.1      iterators_1.0.6    plyr_1.8
>
> [13] RSQLite_0.11.4     sendmailR_1.1-2    stats4_3.1.0       tools_3.1.0
>
> [17] zlibbioc_1.9.0
>
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>
>

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