Couldn't one test for existence by trying to open the BamFile object, and
possibly read one sequence (or maybe just read the header since I guess a
valid bam file can contain zero sequences)?
On Jan 7, 2013 1:32 PM, "Henrik Bengtsson" <h...@biostat.ucsf.edu> wrote:
> 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
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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