On Mon, Jan 7, 2013 at 12:32 PM, Nicolas Delhomme <delho...@embl.de> wrote:
> Hi Martin, Marc,
>
> I'm now implementing the use of BamFile objects in easyRNASeq and I like
> them. I think it would be very useful if when constructing a BamFile the
> existence of the path and index could be tested; i.e. this works:
> BamFile("test.bam","test.bam.bai") although these files do not exist. Is
> there a reason that this validation is not done? If there is, could a
> validation parameter be added (set to FALSE by default to keep the current
> behavior) that would check for the files' existence?
Good idea - I propose argument 'mustExist'.
My $0.02
/Henrik
> The same goes for the yieldSize argument, i.e. this works
> BamFile("test.bam","test.bam.bai",yieldSize=-1), although I'm not sure what a
> -1 yieldSize means. I can of course do these validations within easyRNASeq,
> but anyone else building packages on top of BamFile would probably want to do
> the same...
>
>
> A related point unclear at the moment in the documentation is what the index
> filename should be: i.e. scanBam expects as the index the same value as for
> the bam filename (that assumes the user has not renamed his bam.bai file and
> you never know what users might be doing... :-S ... ) but the BamFile Rd page
> says:
>
> file: A character vector of BAM file paths
> index: A character vector of indices (forBamFile);
>
> so it's unclear to me what the index character vector should contain.
>
> Thanks again for this set of class, they're really handy!
>
> Here's my sessionInfo:
>
> R Under development (unstable) (2012-10-02 r60861)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] Rsamtools_1.11.14 Biostrings_2.27.8 GenomicRanges_1.11.21
> [4] IRanges_1.17.24 BiocGenerics_0.5.6 BiocInstaller_1.9.6
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-5 stats4_2.16.0 tools_2.16.0 zlibbioc_1.5.0
>
> Cheers,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Genome Biology Computational Support
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8310
> Email: nicolas.delho...@embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
>
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